相关论文: pgMAP: a pipeline to enable guide RNA read mapping…

The CMAP (cultural mapping and pattern analysis) visualization toolkit introduced in this paper is an open-source suite for analyzing and visualizing text data - from qualitative fieldnotes and in-depth interview transcripts to historical…

Pipeline parallelism (PP) when training neural networks enables larger models to be partitioned spatially, leading to both lower network communication and overall higher hardware utilization. Unfortunately, to preserve the statistical…

Access to vast amounts of data along with affordable computational power stimulated the reincarnation of neural networks. The progress could not be achieved without adequate software tools, lowering the entry bar for the next generations of…

Short Read Alignment Mapping Metrics (SRAMM): is an efficient and versatile command line tool providing additional short read mapping metrics, filtering, and graphs. Short read aligners report MAPing Quality (MAPQ), but these methods…

Paper maps remain widely used for hiking and sightseeing because they contain curated trails and locally relevant annotations that are often missing from digital navigation applications such as Google Maps. We propose a pipeline to extract…

Recent literature highlights the potential of graph-based approaches within large language model (LLM) retrieval-augmented generation (RAG) pipelines for answering queries of varying complexity, particularly those that fall outside the…

Mapping workflow applications onto parallel platforms is a challenging problem, even for simple application patterns such as pipeline graphs. Several antagonistic criteria should be optimized, such as throughput and latency (or a…

In this paper we introduce a novel parallel pipeline for fast and accurate mapping of RNA sequences on servers equipped with multicore processors. Our software, named HPG-Aligner, leverages the speed of the Burrows-Wheeler Transform to map…

We design and implement a ready-to-use library in PyTorch for performing micro-batch pipeline parallelism with checkpointing proposed by GPipe (Huang et al., 2019). In particular, we develop a set of design components to enable…

Machine learning is a general-purpose technology holding promises for many interdisciplinary research problems. However, significant barriers exist in crossing disciplinary boundaries when most machine learning tools are developed in…

Motivation: Recent advances in sequencing technologies promise ultra-long reads of $\sim$100 kilo bases (kb) in average, full-length mRNA or cDNA reads in high throughput and genomic contigs over 100 mega bases (Mb) in length. Existing…

High throughput genome sequencing technologies such as RNA-Seq and Microarray have the potential to transform clinical decision making and biomedical research by enabling high-throughput measurements of the genome at a granular level.…

We present PEANUT (ParallEl AligNment UTility), a highly parallel GPU-based read mapper with several distinguishing features, including a novel q-gram index (called the q-group index) with small memory footprint built on-the-fly over the…

AutoML systems build machine learning models automatically by performing a search over valid data transformations and learners, along with hyper-parameter optimization for each learner. Many AutoML systems use meta-learning to guide search…

Scaling up deep neural network capacity has been known as an effective approach to improving model quality for several different machine learning tasks. In many cases, increasing model capacity beyond the memory limit of a single…

RNA 3D architectures are stabilized by sophisticated networks of (non-canonical) base pair interactions, which can be conveniently encoded as multi-relational graphs and efficiently exploited by graph theoretical approaches and recent…

Aims. To describe two potential options for the Source Environment Analysis pipeline, SEAPipe, for the Gaia mission. This pipeline will enable the discovery of sources which are new to Gaia, in the sense that they were not found by the…

Multi-hop reading comprehension across multiple documents attracts much attention recently. In this paper, we propose a novel approach to tackle this multi-hop reading comprehension problem. Inspired by human reasoning processing, we…

Mapper, a topological algorithm, is frequently used as an exploratory tool to build a graphical representation of data. This representation can help to gain a better understanding of the intrinsic shape of high-dimensional genomic data and…

We present Piko, a framework for designing, optimizing, and retargeting implementations of graphics pipelines on multiple architectures. Piko programmers express a graphics pipeline by organizing the computation within each stage into…